AutoCloner

Multiple sequence alignment - TraesCS3B01G363500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS3B01G363500	chr3B	100.000	3899	0	0	1	3899	575255251	575259149	0.000000e+00	7201.0
1	TraesCS3B01G363500	chr3A	93.158	2207	105	26	919	3116	578873574	578875743	0.000000e+00	3197.0
2	TraesCS3B01G363500	chr3A	94.254	818	30	7	1	805	578872683	578873496	0.000000e+00	1234.0
3	TraesCS3B01G363500	chr3D	94.885	1525	52	12	1600	3116	438942789	438944295	0.000000e+00	2361.0
4	TraesCS3B01G363500	chr3D	90.111	809	55	17	1	799	438941121	438941914	0.000000e+00	1027.0
5	TraesCS3B01G363500	chr3D	94.858	564	21	2	943	1498	438942114	438942677	0.000000e+00	874.0
6	TraesCS3B01G363500	chr3D	90.385	52	1	1	1522	1573	438942739	438942786	9.040000e-07	65.8
7	TraesCS3B01G363500	chr5D	82.150	1042	159	24	1848	2874	483698315	483699344	0.000000e+00	869.0
8	TraesCS3B01G363500	chr5D	86.047	172	17	6	3430	3599	514150403	514150569	1.110000e-40	178.0
9	TraesCS3B01G363500	chr1A	87.776	679	78	5	2199	2874	452020202	452020878	0.000000e+00	789.0
10	TraesCS3B01G363500	chr1A	88.544	419	46	2	987	1404	500565289	500564872	1.250000e-139	507.0
11	TraesCS3B01G363500	chr1A	92.014	288	23	0	1842	2129	500564360	500564073	4.690000e-109	405.0
12	TraesCS3B01G363500	chr1A	83.911	404	65	0	994	1397	452018570	452018973	1.700000e-103	387.0
13	TraesCS3B01G363500	chr1D	87.706	667	78	4	2211	2874	351247226	351247891	0.000000e+00	774.0
14	TraesCS3B01G363500	chr1D	86.637	681	87	2	2197	2874	405111124	405110445	0.000000e+00	750.0
15	TraesCS3B01G363500	chr1D	89.234	418	44	1	988	1404	405112807	405112390	4.460000e-144	521.0
16	TraesCS3B01G363500	chr1D	91.667	288	24	0	1842	2129	405111873	405111586	2.180000e-107	399.0
17	TraesCS3B01G363500	chr1B	87.407	675	80	5	2203	2874	473824087	473824759	0.000000e+00	771.0
18	TraesCS3B01G363500	chr1B	86.976	668	84	1	2210	2874	544997398	544996731	0.000000e+00	749.0
19	TraesCS3B01G363500	chr1B	89.538	411	42	1	987	1397	544999073	544998664	1.610000e-143	520.0
20	TraesCS3B01G363500	chr1B	91.667	288	24	0	1842	2129	544998179	544997892	2.180000e-107	399.0
21	TraesCS3B01G363500	chr1B	83.911	404	65	0	994	1397	473822301	473822704	1.700000e-103	387.0
22	TraesCS3B01G363500	chr1B	79.259	135	22	4	3178	3312	662824614	662824486	5.370000e-14	89.8
23	TraesCS3B01G363500	chr4A	80.469	1024	182	12	1852	2872	596625633	596624625	0.000000e+00	767.0
24	TraesCS3B01G363500	chr4A	84.127	252	32	6	3432	3679	31397183	31396936	1.810000e-58	237.0
25	TraesCS3B01G363500	chr6A	86.706	677	85	3	2210	2883	115946944	115947618	0.000000e+00	747.0
26	TraesCS3B01G363500	chrUn	83.292	401	65	2	997	1396	126673962	126674361	6.150000e-98	368.0
27	TraesCS3B01G363500	chr5A	83.042	401	66	2	997	1396	691671083	691670684	2.860000e-96	363.0
28	TraesCS3B01G363500	chr5A	83.908	261	35	5	3424	3680	38147650	38147907	3.890000e-60	243.0
29	TraesCS3B01G363500	chr2B	84.806	283	43	0	1847	2129	59180004	59180286	6.380000e-73	285.0
30	TraesCS3B01G363500	chr7D	83.094	278	47	0	1852	2129	573692842	573693119	1.800000e-63	254.0
31	TraesCS3B01G363500	chr6D	83.539	243	36	3	3432	3673	71936324	71936563	1.410000e-54	224.0
32	TraesCS3B01G363500	chr4D	80.000	280	56	0	1852	2131	6898537	6898816	1.420000e-49	207.0
33	TraesCS3B01G363500	chr5B	84.043	188	30	0	3712	3899	303602852	303602665	8.610000e-42	182.0
34	TraesCS3B01G363500	chr5B	81.761	159	29	0	3741	3899	303600985	303601143	2.440000e-27	134.0
35	TraesCS3B01G363500	chr7B	82.540	189	31	2	3712	3899	161239174	161238987	8.670000e-37	165.0

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS3B01G363500	chr3B	575255251	575259149	3898	False	7201.000000	7201	100.000000	1	3899	1	chr3B.!!$F1	3898
1	TraesCS3B01G363500	chr3A	578872683	578875743	3060	False	2215.500000	3197	93.706000	1	3116	2	chr3A.!!$F1	3115
2	TraesCS3B01G363500	chr3D	438941121	438944295	3174	False	1081.950000	2361	92.559750	1	3116	4	chr3D.!!$F1	3115
3	TraesCS3B01G363500	chr5D	483698315	483699344	1029	False	869.000000	869	82.150000	1848	2874	1	chr5D.!!$F1	1026
4	TraesCS3B01G363500	chr1A	452018570	452020878	2308	False	588.000000	789	85.843500	994	2874	2	chr1A.!!$F1	1880
5	TraesCS3B01G363500	chr1A	500564073	500565289	1216	True	456.000000	507	90.279000	987	2129	2	chr1A.!!$R1	1142
6	TraesCS3B01G363500	chr1D	351247226	351247891	665	False	774.000000	774	87.706000	2211	2874	1	chr1D.!!$F1	663
7	TraesCS3B01G363500	chr1D	405110445	405112807	2362	True	556.666667	750	89.179333	988	2874	3	chr1D.!!$R1	1886
8	TraesCS3B01G363500	chr1B	473822301	473824759	2458	False	579.000000	771	85.659000	994	2874	2	chr1B.!!$F1	1880
9	TraesCS3B01G363500	chr1B	544996731	544999073	2342	True	556.000000	749	89.393667	987	2874	3	chr1B.!!$R2	1887
10	TraesCS3B01G363500	chr4A	596624625	596625633	1008	True	767.000000	767	80.469000	1852	2872	1	chr4A.!!$R2	1020
11	TraesCS3B01G363500	chr6A	115946944	115947618	674	False	747.000000	747	86.706000	2210	2883	1	chr6A.!!$F1	673

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
284	297	1.008538	GTCTTGTGCCCGCACTTTG	60.009	57.895	19.77	10.25	46.30	2.77	F
829	893	1.103398	AAGCCCCATGTATCGCTTGC	61.103	55.000	5.35	0.00	39.98	4.01	F
830	894	1.526917	GCCCCATGTATCGCTTGCT	60.527	57.895	0.00	0.00	0.00	3.91	F
2610	4339	1.663695	CCAACAACGTGAAGTCCAGT	58.336	50.000	0.00	0.00	0.00	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1598	1760	1.889829	CTTATTTGGTGGGCCGACAAA	59.110	47.619	22.30	22.30	38.33	2.83	R
2610	4339	2.662596	GGCGGGATGTCACAGACA	59.337	61.111	1.95	1.95	46.90	3.41	R
2856	4585	3.481453	CTGATCCTCATCCTCGTACTCA	58.519	50.000	0.00	0.00	0.00	3.41	R
3730	5459	0.035152	ATCGCCATCAAGTTGCTGGA	60.035	50.000	26.23	9.40	35.77	3.86	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
178	190	3.000819	CCACCACACCGCCTCCTA	61.001	66.667	0.00	0.00	0.00	2.94
270	283	4.377897	CACGGTCTTTCTTTACCAGTCTT	58.622	43.478	0.00	0.00	35.35	3.01
271	284	4.211374	CACGGTCTTTCTTTACCAGTCTTG	59.789	45.833	0.00	0.00	35.35	3.02
284	297	1.008538	GTCTTGTGCCCGCACTTTG	60.009	57.895	19.77	10.25	46.30	2.77
324	337	6.061022	TGCTGTAAGTCTGGATTTGGAATA	57.939	37.500	0.00	0.00	35.30	1.75
473	488	7.776030	TCTGTAGTTCTCTCTATTCTAGGTTGG	59.224	40.741	0.00	0.00	0.00	3.77
475	490	7.776030	TGTAGTTCTCTCTATTCTAGGTTGGAG	59.224	40.741	0.00	0.00	0.00	3.86
488	503	3.335579	AGGTTGGAGTACTTCGATTTGC	58.664	45.455	0.00	0.00	0.00	3.68
563	578	1.844289	TCCGGCCCCTTGTTACTGT	60.844	57.895	0.00	0.00	0.00	3.55
821	885	1.140312	GGGATCTGAAGCCCCATGTA	58.860	55.000	7.53	0.00	46.16	2.29
823	887	2.290577	GGGATCTGAAGCCCCATGTATC	60.291	54.545	7.53	0.00	46.16	2.24
829	893	1.103398	AAGCCCCATGTATCGCTTGC	61.103	55.000	5.35	0.00	39.98	4.01
830	894	1.526917	GCCCCATGTATCGCTTGCT	60.527	57.895	0.00	0.00	0.00	3.91
837	901	3.681897	CCATGTATCGCTTGCTTAGATCC	59.318	47.826	0.00	0.00	0.00	3.36
845	909	2.936498	GCTTGCTTAGATCCGTGCTTTA	59.064	45.455	0.00	0.00	0.00	1.85
853	917	7.039993	TGCTTAGATCCGTGCTTTACTGATATA	60.040	37.037	0.00	0.00	33.96	0.86
854	918	7.273815	GCTTAGATCCGTGCTTTACTGATATAC	59.726	40.741	0.00	0.00	33.96	1.47
855	919	5.700846	AGATCCGTGCTTTACTGATATACG	58.299	41.667	0.00	0.00	33.96	3.06
856	920	5.472478	AGATCCGTGCTTTACTGATATACGA	59.528	40.000	0.00	0.00	33.96	3.43
857	921	4.852138	TCCGTGCTTTACTGATATACGAC	58.148	43.478	0.00	0.00	32.36	4.34
858	922	3.979495	CCGTGCTTTACTGATATACGACC	59.021	47.826	0.00	0.00	32.36	4.79
859	923	4.261489	CCGTGCTTTACTGATATACGACCT	60.261	45.833	0.00	0.00	32.36	3.85
860	924	4.675565	CGTGCTTTACTGATATACGACCTG	59.324	45.833	0.00	0.00	32.36	4.00
861	925	5.505159	CGTGCTTTACTGATATACGACCTGA	60.505	44.000	0.00	0.00	32.36	3.86
862	926	6.270815	GTGCTTTACTGATATACGACCTGAA	58.729	40.000	0.00	0.00	0.00	3.02

Showing 1 to 25 of 487 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	7.461749	TGAGTAAATTTGAAATCTCCCACTCT	58.538	34.615	0.00	0.00	32.03	3.24
16	17	7.010160	ACCTTGAGTAAATTTGAAATCTCCCA	58.990	34.615	0.00	0.00	0.00	4.37
251	264	4.023963	GCACAAGACTGGTAAAGAAAGACC	60.024	45.833	0.00	0.00	36.17	3.85
255	268	3.219281	GGGCACAAGACTGGTAAAGAAA	58.781	45.455	0.00	0.00	0.00	2.52
271	284	0.887387	TAAGGACAAAGTGCGGGCAC	60.887	55.000	15.68	15.68	46.50	5.01
284	297	7.603024	ACTTACAGCATCAAAAGTACTAAGGAC	59.397	37.037	0.00	0.00	30.62	3.85
324	337	3.770666	CAACTACTCGAATCACCGTGAT	58.229	45.455	8.28	8.28	39.09	3.06
473	488	2.877335	ACGGAGCAAATCGAAGTACTC	58.123	47.619	0.00	0.00	0.00	2.59
475	490	2.991190	TGAACGGAGCAAATCGAAGTAC	59.009	45.455	0.00	0.00	0.00	2.73
488	503	6.020281	CAGATCTAAGAAACGATTGAACGGAG	60.020	42.308	0.00	0.00	37.61	4.63
668	687	7.010552	CACCAGATCTTCTAAACAATAACTCGG	59.989	40.741	0.00	0.00	0.00	4.63
674	693	5.116180	CGCCACCAGATCTTCTAAACAATA	58.884	41.667	0.00	0.00	0.00	1.90
680	699	0.901827	TGCGCCACCAGATCTTCTAA	59.098	50.000	4.18	0.00	0.00	2.10
682	701	1.078848	GTGCGCCACCAGATCTTCT	60.079	57.895	4.18	0.00	0.00	2.85
821	885	1.858091	CACGGATCTAAGCAAGCGAT	58.142	50.000	0.00	0.00	0.00	4.58
823	887	0.807667	AGCACGGATCTAAGCAAGCG	60.808	55.000	0.00	0.00	0.00	4.68
829	893	7.482113	CGTATATCAGTAAAGCACGGATCTAAG	59.518	40.741	0.00	0.00	40.67	2.18
830	894	7.173735	TCGTATATCAGTAAAGCACGGATCTAA	59.826	37.037	0.00	0.00	40.67	2.10
837	901	4.675565	CAGGTCGTATATCAGTAAAGCACG	59.324	45.833	0.00	0.00	0.00	5.34
845	909	5.833667	TGAGGATTTCAGGTCGTATATCAGT	59.166	40.000	0.00	0.00	0.00	3.41
853	917	5.420409	GAACTAATGAGGATTTCAGGTCGT	58.580	41.667	0.00	0.00	39.68	4.34
854	918	4.504461	CGAACTAATGAGGATTTCAGGTCG	59.496	45.833	0.00	0.00	39.68	4.79
855	919	5.420409	ACGAACTAATGAGGATTTCAGGTC	58.580	41.667	0.00	0.00	39.68	3.85
856	920	5.422214	ACGAACTAATGAGGATTTCAGGT	57.578	39.130	0.00	0.00	39.68	4.00
857	921	7.843490	TTTACGAACTAATGAGGATTTCAGG	57.157	36.000	0.00	0.00	39.68	3.86

Showing 1 to 25 of 495 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.